Ecology and Evolution of Lichens and Associated Microorganisms

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Environmental and Ecological Interactions of Fungi".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 23817

Special Issue Editors


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Guest Editor
Commonwealth Scientific and Industrial Research Organization, Melbourne, Australia
Interests: lichens and associated microorganisms

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Guest Editor
Senckenberg Biodiversität und Klima Forschungszentrumdisabled, Frankfurt am Main, Germany
Interests: ecology; evolution and chemistry of lichenized fungi

Special Issue Information

Dear Colleagues,

Lichens, a symbiotic association between a fungus and one or more photosynthetic partners, are among the evolutionarily most successful symbiotic systems. Their broad ecological range and the high species diversity for the fungal partner demonstrates their extraordinary evolutionary success. The understanding of biological processes and eco-evolutionary dynamics of lichen symbionts has been greatly assisted by next-generation sequencing approaches which provide deeper insights into genome architecture.

In this Special Issue of Journal of Fungi entitled “Ecology and evolution of lichens and associated microorganisms”, we aim to bring together exciting new research contributing to progress and advancements in various areas, such as lichen ecology, evolution and taxonomy. We welcome manuscripts presenting original research addressing consequential questions as well as theoretical investigations that advance our understanding of the following topics through extensive research in these areas. 

Dr. Cecile Gueidan
Dr. Garima Singh
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • ecology and evolution of lichens and associated microorganisms
  • population genetics and genomics of lichens and associated microorganisms
  • molecular phylogenetics and phylogenomics of lichenized fungi
  • metagenomic and metabarcoding of lichens and associated microorganisms

Published Papers (9 papers)

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Research

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19 pages, 6045 KiB  
Article
Survey of Lichenized Fungi DNA Barcodes on King George Island (Antarctica): An Aid to Species Discovery
by Renato Daniel La Torre, Daniel Ramos, Mayra Doris Mejía, Edgar Neyra, Edwin Loarte and Gisella Orjeda
J. Fungi 2023, 9(5), 552; https://doi.org/10.3390/jof9050552 - 11 May 2023
Viewed by 1912
Abstract
DNA barcoding is a powerful method for the identification of lichenized fungi groups for which the diversity is already well-represented in nucleotide databases, and an accurate, robust taxonomy has been established. However, the effectiveness of DNA barcoding for identification is expected to be [...] Read more.
DNA barcoding is a powerful method for the identification of lichenized fungi groups for which the diversity is already well-represented in nucleotide databases, and an accurate, robust taxonomy has been established. However, the effectiveness of DNA barcoding for identification is expected to be limited for understudied taxa or regions. One such region is Antarctica, where, despite the importance of lichens and lichenized fungi identification, their genetic diversity is far from characterized. The aim of this exploratory study was to survey the lichenized fungi diversity of King George Island using a fungal barcode marker as an initial identification tool. Samples were collected unrestricted to specific taxa in coastal areas near Admiralty Bay. Most samples were identified using the barcode marker and verified up to the species or genus level with a high degree of similarity. A posterior morphological evaluation focused on samples with novel barcodes allowed for the identification of unknown Austrolecia, Buellia, and Lecidea s.l. species. These results contribute to better represent the lichenized fungi diversity in understudied regions such as Antarctica by increasing the richness of the nucleotide databases. Furthermore, the approach used in this study is valuable for exploratory surveys in understudied regions to guide taxonomic efforts towards species recognition and discovery. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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18 pages, 5127 KiB  
Article
Fungal Diversity Associated with Thirty-Eight Lichen Species Revealed a New Genus of Endolichenic Fungi, Intumescentia gen. nov. (Teratosphaeriaceae)
by Hongli Si, Yichen Wang, Yanyu Liu, Shiguo Li, Tanay Bose and Runlei Chang
J. Fungi 2023, 9(4), 423; https://doi.org/10.3390/jof9040423 - 29 Mar 2023
Cited by 1 | Viewed by 2539
Abstract
Fungi from the Teratosphaeriaceae (Mycosphaerellales; Dothideomycetes; Ascomycota) have a wide range of lifestyles. Among these are a few species that are endolichenic fungi. However, the known diversity of endolichenic fungi from Teratosphaeriaceae is far less understood compared to other lineages of Ascomycota. We [...] Read more.
Fungi from the Teratosphaeriaceae (Mycosphaerellales; Dothideomycetes; Ascomycota) have a wide range of lifestyles. Among these are a few species that are endolichenic fungi. However, the known diversity of endolichenic fungi from Teratosphaeriaceae is far less understood compared to other lineages of Ascomycota. We conducted five surveys from 2020 to 2021 in Yunnan Province of China, to explore the biodiversity of endolichenic fungi. During these surveys, we collected multiple samples of 38 lichen species. We recovered a total of 205 fungal isolates representing 127 species from the medullary tissues of these lichens. Most of these isolates were from Ascomycota (118 species), and the remaining were from Basidiomycota (8 species) and Mucoromycota (1 species). These endolichenic fungi represented a wide variety of guilds, including saprophytes, plant pathogens, human pathogens, as well as entomopathogenic, endolichenic, and symbiotic fungi. Morphological and molecular data indicated that 16 of the 206 fungal isolates belonged to the family Teratosphaeriaceae. Among these were six isolates that had a low sequence similarity with any of the previously described species of Teratosphaeriaceae. For these six isolates, we amplified additional gene regions and conducted phylogenetic analyses. In both single gene and multi-gene phylogenetic analyses using ITS, LSU, SSU, RPB2, TEF1, ACT, and CAL data, these six isolates emerged as a monophyletic lineage within the family Teratosphaeriaceae and sister to a clade that included fungi from the genera Acidiella and Xenopenidiella. The analyses also indicated that these six isolates represented four species. Therefore, we established a new genus, Intumescentia gen. nov., to describe these species as Intumescentia ceratinae, I. tinctorum, I. pseudolivetorum, and I. vitii. These four species are the first endolichenic fungi representing Teratosphaeriaceae from China. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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13 pages, 2295 KiB  
Article
Biological Crust Diversity Related to Elevation and Soil Properties at Local Scale in a Montane Scrub of Ecuador
by Leslye Ruiz, Vinicio Carrión-Paladines, Marlon Vega, Fausto López and Ángel Benítez
J. Fungi 2023, 9(3), 386; https://doi.org/10.3390/jof9030386 - 22 Mar 2023
Cited by 1 | Viewed by 2076
Abstract
The montane shrublands of southern Ecuador represent one of the least studied ecosystems, which in the last decade have been seriously threatened by increasing wildfires, deforestation, overgrazing, and conversion to forest plantations. Our main objective was to determine, at the local scale, the [...] Read more.
The montane shrublands of southern Ecuador represent one of the least studied ecosystems, which in the last decade have been seriously threatened by increasing wildfires, deforestation, overgrazing, and conversion to forest plantations. Our main objective was to determine, at the local scale, the diversity of species composing the biological soil crust (BSC) at three elevations (2100, 2300, and 2500 m.a.s.l.) and their possible relationships with soil physical and chemical properties in montane shrublands. For this purpose, three monitoring plots of 100 m2 were established at each elevation, and within each plot, 20 subplots were established (180 subplots sampled in total). In addition, composite soil samples were collected at a depth of 0 to 10 cm, and some physical and biochemical parameters (e.g., bulk density, texture, pH, organic matter, soil organic carbon, total nitrogen, available phosphorus, and potassium) of the soil were analyzed. The results show 35 species (23 lichens, 10 bryophytes and 2 cyanobacteria) at three elevations with a bell-shaped or hump-shaped distribution pattern. This allowed us to point out that the species richness was higher at the intermediate elevations and that the composition showed significant differences in the three elevations related to soil factors. Elevation and soil drivers may help to better chose the more suitable biological soil crust (lichen-dominated and bryophyte-dominated BSC) for the management and conservation of the montane scrub of Ecuador, which is strongly threatened by human activities. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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18 pages, 3702 KiB  
Article
High Andean Steppes of Southern Chile Contain Little-Explored Peltigera Lichen Symbionts
by Karla Veas-Mattheos, Katerin Almendras, Matías Pezoa, Cecilia Muster and Julieta Orlando
J. Fungi 2023, 9(3), 372; https://doi.org/10.3390/jof9030372 - 18 Mar 2023
Cited by 1 | Viewed by 1545
Abstract
Peltigera lichens can colonize extreme habitats, such as high-elevation ecosystems, but their biodiversity is still largely unknown in these environments, especially in the southern hemi- sphere. We assessed the genetic diversity of mycobionts and cyanobionts of 60 Peltigera lichens collected in three high [...] Read more.
Peltigera lichens can colonize extreme habitats, such as high-elevation ecosystems, but their biodiversity is still largely unknown in these environments, especially in the southern hemi- sphere. We assessed the genetic diversity of mycobionts and cyanobionts of 60 Peltigera lichens collected in three high Andean steppes of southern Chile using LSU, β-tubulin, COR3 and ITS loci for mycobionts, and SSU and rbcLX loci for cyanobionts. We obtained 240 sequences for the different mycobiont markers and 118 for the cyanobiont markers, including the first report of β-tubulin sequences of P. patagonica through modifying a previously designed primer. Phylogenetic analyses, ITS scrutiny and variability of haplotypes were used to compare the sequences with those previously reported. We found seven mycobiont species and eleven cyanobiont haplotypes, including considerable novel symbionts. This was reflected by ~30% of mycobionts and ~20% of cyanobionts haplotypes that yielded less than 99% BLASTn sequence identity, 15 new sequences of the ITS1-HR, and a putative new Peltigera species associated with 3 Nostoc haplotypes not previously reported. Our results suggest that high Andean steppe ecosystems are habitats of unknown or little-explored lichen species and thus valuable environments to enhance our understanding of global Peltigera biodiversity. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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10 pages, 849 KiB  
Article
Fungal Host Affects Photosynthesis in a Lichen Holobiont
by Meike Schulz, Imke Schmitt, Daniel Weber and Francesco Dal Grande
J. Fungi 2022, 8(12), 1267; https://doi.org/10.3390/jof8121267 - 30 Nov 2022
Cited by 2 | Viewed by 1452
Abstract
Corals and lichens are iconic examples of photosynthetic holobionts, i.e., ecological and evolutionary units resulting from the tightly integrated association of algae and prokaryotic microbiota with animal or fungal hosts, respectively. While the role of the coral host in modulating photosynthesis has been [...] Read more.
Corals and lichens are iconic examples of photosynthetic holobionts, i.e., ecological and evolutionary units resulting from the tightly integrated association of algae and prokaryotic microbiota with animal or fungal hosts, respectively. While the role of the coral host in modulating photosynthesis has been clarified to a large extent in coral holobionts, the role of the fungal host in this regard is far less understood. Here, we address this question by taking advantage of the recent discovery of highly specific fungal–algal pairings corresponding to climatically adapted ecotypes of the lichen-forming genus Umbilicaria. Specifically, we compared chlorophyll a fluorescence kinetics among lichen thalli consisting of different fungal–algal combinations. We show that photosynthetic performance in these lichens is not only driven by algal genotype, but also by fungal host species identity and intra-host genotype. These findings shed new light on the closely intertwined physiological processes of fungal and algal partners in the lichen symbiosis. Indeed, the specific combinations of fungal and algal genotypes within a lichen individual—and the resulting combined functional phenotype—can be regarded as a response to the environment. Our findings suggest that characterizing the genetic composition of both eukaryotic partners is an important complimentary step to understand and predict the lichen holobiont’s responses to environmental change. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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17 pages, 4741 KiB  
Article
Microbiomic Analysis of Bacteria Associated with Rock Tripe Lichens in Continental and Maritime Antarctic Regions
by Zichen He, Takeshi Naganuma, Ryosuke Nakai, Satoshi Imura, Megumu Tsujimoto and Peter Convey
J. Fungi 2022, 8(8), 817; https://doi.org/10.3390/jof8080817 - 03 Aug 2022
Cited by 5 | Viewed by 3515
Abstract
Increased research attention is being given to bacterial diversity associated with lichens. Rock tripe lichens (Umbilicariaceae) were collected from two distinct Antarctic biological regions, the continental region near the Japanese Antarctic station (Syowa Station) and the maritime Antarctic South Orkney Islands [...] Read more.
Increased research attention is being given to bacterial diversity associated with lichens. Rock tripe lichens (Umbilicariaceae) were collected from two distinct Antarctic biological regions, the continental region near the Japanese Antarctic station (Syowa Station) and the maritime Antarctic South Orkney Islands (Signy Island), in order to compare their bacterial floras and potential metabolism. Bulk DNA extracted from the lichen samples was used to amplify the 18S rRNA gene and the V3-V4 region of the 16S rRNA gene, whose amplicons were Sanger- and MiSeq-sequenced, respectively. The fungal and algal partners represented members of the ascomycete genus Umbilicaria and the green algal genus Trebouxia, based on 18S rRNA gene sequences. The V3-V4 sequences were grouped into operational taxonomic units (OTUs), which were assigned to eight bacterial phyla, Acidobacteriota, Actinomyceota, Armatimonadota, Bacteroidota, Cyanobacteria, Deinococcota, Pseudomonadota and the candidate phylum Saccharibacteria (also known as TM7), commonly present in all samples. The OTU floras of the two biological regions were clearly distinct, with regional biomarker genera, such as Mucilaginibacter and Gluconacetobacter, respectively. The OTU-based metabolism analysis predicted higher membrane transport activities in the maritime Antarctic OTUs, probably influenced by the sampling area’s warmer maritime climatic setting. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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25 pages, 1645 KiB  
Article
High Diversity of Type I Polyketide Genes in Bacidia rubella as Revealed by the Comparative Analysis of 23 Lichen Genomes
by Julia V. Gerasimova, Andreas Beck, Silke Werth and Philipp Resl
J. Fungi 2022, 8(5), 449; https://doi.org/10.3390/jof8050449 - 26 Apr 2022
Cited by 11 | Viewed by 2811
Abstract
Fungi involved in lichen symbioses produce a large array of secondary metabolites that are often diagnostic in the taxonomic delimitation of lichens. The most common lichen secondary metabolites—polyketides—are synthesized by polyketide synthases, particularly by Type I PKS (TI-PKS). Here, we present a comparative [...] Read more.
Fungi involved in lichen symbioses produce a large array of secondary metabolites that are often diagnostic in the taxonomic delimitation of lichens. The most common lichen secondary metabolites—polyketides—are synthesized by polyketide synthases, particularly by Type I PKS (TI-PKS). Here, we present a comparative genomic analysis of the TI-PKS gene content of 23 lichen-forming fungal genomes from Ascomycota, including the de novo sequenced genome of Bacidia rubella. Firstly, we identify a putative atranorin cluster in B. rubella. Secondly, we provide an overview of TI-PKS gene diversity in lichen-forming fungi, and the most comprehensive Type I PKS phylogeny of lichen-forming fungi to date, including 624 sequences. We reveal a high number of biosynthetic gene clusters and examine their domain composition in the context of previously characterized genes, confirming that PKS genes outnumber known secondary substances. Moreover, two novel groups of reducing PKSs were identified. Although many PKSs remain without functional assignments, our findings highlight that genes from lichen-forming fungi represent an untapped source of novel polyketide compounds. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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16 pages, 3533 KiB  
Article
An Exception to the Rule? Could Photobiont Identity Be a Better Predictor of Lichen Phenotype than Mycobiont Identity?
by Jana Steinová, Håkon Holien, Alica Košuthová and Pavel Škaloud
J. Fungi 2022, 8(3), 275; https://doi.org/10.3390/jof8030275 - 09 Mar 2022
Cited by 5 | Viewed by 2985
Abstract
With rare exceptions, the shape and appearance of lichen thalli are determined by the fungal partner; thus, mycobiont identity is normally used for lichen identification. However, it has repeatedly been shown in recent decades that phenotypic data often does not correspond with fungal [...] Read more.
With rare exceptions, the shape and appearance of lichen thalli are determined by the fungal partner; thus, mycobiont identity is normally used for lichen identification. However, it has repeatedly been shown in recent decades that phenotypic data often does not correspond with fungal gene evolution. Here, we report such a case in a three-species complex of red-fruited Cladonia lichens, two of which clearly differ morphologically, chemically, ecologically and in distribution range. We analysed 64 specimens of C. bellidiflora, C. polydactyla and C. umbricola, mainly collected in Europe, using five variable mycobiont-specific and two photobiont-specific molecular markers. All mycobiont markers exhibited very low variability and failed to separate the species. In comparison, photobiont identity corresponded better with lichen phenotype and separated esorediate C. bellidiflora from the two sorediate taxa. These results can be interpreted either as an unusual case of lichen photomorphs or as an example of recent speciation, in which phenotypic differentiation precedes the separation of the molecular markers. We hypothesise that association with different photobionts, which is probably related to habitat differentiation, may have triggered speciation in the mycobiont species. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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Review

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15 pages, 1867 KiB  
Review
Linking Lichen Metabolites to Genes: Emerging Concepts and Lessons from Molecular Biology and Metagenomics
by Garima Singh
J. Fungi 2023, 9(2), 160; https://doi.org/10.3390/jof9020160 - 25 Jan 2023
Cited by 11 | Viewed by 2334
Abstract
Lichen secondary metabolites have tremendous pharmaceutical and industrial potential. Although more than 1000 metabolites have been reported from lichens, less than 10 have been linked to the genes coding them. The current biosynthetic research focuses strongly on linking molecules to genes as this [...] Read more.
Lichen secondary metabolites have tremendous pharmaceutical and industrial potential. Although more than 1000 metabolites have been reported from lichens, less than 10 have been linked to the genes coding them. The current biosynthetic research focuses strongly on linking molecules to genes as this is fundamental to adapting the molecule for industrial application. Metagenomic-based gene discovery, which bypasses the challenges associated with culturing an organism, is a promising way forward to link secondary metabolites to genes in non-model, difficult-to-culture organisms. This approach is based on the amalgamation of the knowledge of the evolutionary relationships of the biosynthetic genes, the structure of the target molecule, and the biosynthetic machinery required for its synthesis. So far, metagenomic-based gene discovery is the predominant approach by which lichen metabolites have been linked to their genes. Although the structures of most of the lichen secondary metabolites are well-documented, a comprehensive review of the metabolites linked to their genes, strategies implemented to establish this link, and crucial takeaways from these studies is not available. In this review, I address the following knowledge gaps and, additionally, provide critical insights into the results of these studies, elaborating on the direct and serendipitous lessons that we have learned from them. Full article
(This article belongs to the Special Issue Ecology and Evolution of Lichens and Associated Microorganisms)
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